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Simplifying Chemical Reaction Network Implementations with Two-Stranded DNA Building Blocks

Authors Robert F. Johnson , Lulu Qian

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Author Details

Robert F. Johnson
  • California Institute of Technology, Pasadena, CA, USA
Lulu Qian
  • California Institute of Technology, Pasadena, CA, USA

Funding

  • Johnson, Robert F.: NSF Graduate Research Fellowship.
  • Qian, Lulu: NSF grant CCF-1908643.

Acknowledgements

We would like to thank Chris Thachuk and Erik Winfree for helpful discussions on new DNA strand displacement motifs and optimization thereof.

Cite As Get BibTex

Robert F. Johnson and Lulu Qian. Simplifying Chemical Reaction Network Implementations with Two-Stranded DNA Building Blocks. In 26th International Conference on DNA Computing and Molecular Programming (DNA 26). Leibniz International Proceedings in Informatics (LIPIcs), Volume 174, pp. 2:1-2:14, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2020) https://doi.org/10.4230/LIPIcs.DNA.2020.2

Abstract

In molecular programming, the Chemical Reaction Network model is often used to describe real or hypothetical systems. Often, an interesting computational task can be done with a known hypothetical Chemical Reaction Network, but often such networks have no known physical implementation. One of the important breakthroughs in the field was that any Chemical Reaction Network can be physically implemented, approximately, using DNA strand displacement mechanisms. This allows us to treat the Chemical Reaction Network model as a programming language and the implementation schemes as its compiler. This also suggests that it would be useful to optimize the result of such a compilation, and in general to find effective ways to design better DNA strand displacement systems.
We discuss DNA strand displacement systems in terms of "motifs", short sequences of elementary DNA strand displacement reactions. We argue that describing such motifs in terms of their inputs and outputs, then building larger systems out of the abstracted motifs, can be an efficient way of designing DNA strand displacement systems. We discuss four previously studied motifs in this abstracted way, and present a new motif based on cooperative 4-way strand exchange. We then show how Chemical Reaction Network implementations can be built out of abstracted motifs, discussing existing implementations as well as presenting two new implementations based on 4-way strand exchange, one of which uses the new cooperative motif. The new implementations both have two desirable properties not found in existing implementations, namely both use only at most 2-stranded DNA complexes for signal and fuel complexes and both are physically reversible. There are reasons to believe that those properties may make them more robust and energy-efficient, but at the expense of using more fuel complexes than existing implementation schemes.

Subject Classification

ACM Subject Classification
  • Computer systems organization → Molecular computing
Keywords
  • Molecular programming
  • DNA computing
  • Chemical Reaction Networks
  • DNA strand displacement

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